Staff Sergeant Frank Wuterich, a squad leader and the alleged ringleader, was charged with 13 counts of murder. He is accused of ordering Marines under his charge to “shoot first and ask questions later” on entering a house.

Sergeant Wuterich, 26 was also charged with making a false official statement and soliciting another sergeant to make false official statements. He faces a maximum penalty of life in prison for his alleged role.

The charges did not allege premeditated murder, according to Mark Zaid, an attorney for Sergeant Wuterich. Mr Zaid said that his client would not be executed if found guilty. “The death penalty is not on the table,” he said.

But they underlined the seriousness with which the Pentagon is pursuing one of the darkest episodes for the American military in Iraq. It has drawn comparisons with the notorious civilian massacre at My Lai in Vietnam in 1968.

The Haditha killings, which occurred on November 19, 2005, triggered the biggest criminal investigation of US troops in Iraq in terms of Iraqis killed. Nouri al-Maliki, the Prime Minister, has called the deaths a “terrible crime”.

The highest ranking defendant, Lieutenant-Colonel Jeffrey Chessani, 42, was accused of failing to obey an order or regulation, encompassing dereliction of duty. The other officers charged were First Lieutenant Andrew Grayson, 25, Captain Lucas McConnell, 31, and Captain Randy Stone, 34, a military attorney.

At the time of the killings, the US military initially said that 15 Iraqi civilians had died after being hit by a roadside bomb, and that Marines then killed eight insurgents in an ensuing firefight.

There was no full US investigation into what happened until three months after when video footage taken by a local human rights activist was passed to Time magazine.

A parallel military investigation has examined whether officers in the Marines’ chain of command tried to cover up the events. Results of that inquiry have not been made public.

The shootings occurred after a roadside bomb rocked a Marine patrol, killing one Marine and injuring two others. Haditha sits in Anbar province, the heart of the Sunni insurgency.

It has since emerged that after the Marine was killed by the bomb, five Iraqi civilians were shot as they approached the scene in a taxi.

Others, including women and children, died after Marines opened fire on houses over a course of three hours. The dead included a three-year-old child, several women and a man of 76. Local people say that no bullets were fired other than by the troops.

The Marines’ lawyers deny that the men engaged in pre-meditated killing. They are expected to argue that civilians were killed in the crossfire of a battle as the Marines attempted to defend themselves from a perceived threat.

Sergeant Wuterich was at the centre of the military investigation into the incident. All the soldiers were based at Camp Pendleton near San Diego, California, and remained in combat for months after the incident.

Defence lawyers have said that under military rules of engagement, it can be permissible for Marines to clear houses with grenades and guns if they believe that the occupants are threatening their lives.

Neal Puckett, a defence attorney, said that Sergeant Wuterich would deny the charges. Part of his defence would be that he was doing what he had been trained to do. “Staff Sergeant Wuterich is not guilty in these charges and acted lawfully,” he said.

Because many US troops are involved, it is expected that prosecutors will seek to offer plea deals to some in return for testimony against the others.

In Iraq the news of the indictments was received with scepticism. “The trial they are talking about is fake,” said Naji al-Ani, 36, a labourer in Haditha.

“The troops should be brought here, in front of an Iraqi court. They committed a horrible crime against innocents.”